ProteinAtlas MCP Server

Instructions

Implementation Reference

• src/index.ts:982-1008 (handler)

  The main handler function for the 'get_brain_expression' tool. Validates input using isValidGeneArgs, fetches brain expression data via fetchBrainExpression, and returns formatted JSON response or error.

  private async handleGetBrainExpression(args: any) {
    if (!isValidGeneArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid gene arguments');
    }
  
    try {
      const result = await this.fetchBrainExpression(args.gene);
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(result, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error fetching brain expression: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:522-533 (registration)

  Tool registration in the listTools response, including name, description, and input schema definition.

  {
    name: 'get_brain_expression',
    description: 'Get brain region expression data for a protein',
    inputSchema: {
      type: 'object',
      properties: {
        gene: { type: 'string', description: 'Gene symbol' },
        format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' },
      },
      required: ['gene'],
    },
  },

• src/index.ts:525-532 (schema)

  Input schema defining parameters for the get_brain_expression tool: required 'gene' string and optional 'format'.

  inputSchema: {
    type: 'object',
    properties: {
      gene: { type: 'string', description: 'Gene symbol' },
      format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' },
    },
    required: ['gene'],
  },

• src/index.ts:768-771 (helper)

  Helper method that performs the API query to Human Protein Atlas with specific columns for brain tissue expression data.

  private async fetchBrainExpression(gene: string): Promise<any> {
    const columns = ['g', 'eg', 'rnabrs', 'rnabrd', 'rnabrss', 'brain_RNA_amygdala', 'brain_RNA_cerebellum', 'brain_RNA_cerebral_cortex', 'brain_RNA_hippocampal_formation', 'brain_RNA_hypothalamus'];
    return this.searchProteins(gene, 'json', columns, 1);
  }

• src/index.ts:63-73 (helper)

  Input validation helper function used by get_brain_expression and similar tools to validate gene and optional format arguments.

  const isValidGeneArgs = (
    args: any
  ): args is { gene: string; format?: string } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.gene === 'string' &&
      args.gene.length > 0 &&
      (args.format === undefined || ['json', 'tsv', 'xml', 'trig'].includes(args.format))
    );
  };